fitBayes uses Bayesian MCMC to sample terminal states (species means) as well as the parameters of an evolutionary model from their joint posterior distribution, following Revell & Reynolds (2012).
fitBayes(tree, x, ngen=10000, model="BM", method="reduced", control=list())An object of class "fitBayes" that includes a matrix (mcmc) with a number of rows ngen/control$sample+1 containing the posterior sample and likelihoods.
Matrix columns are labeled by species (for species means and variances), or by the corresponding evolutionary parameter.
an object of class "phylo".
a vector of phenotypic values for individuals; names(x) should contain the species names (not individual IDs).
a integer indicating the number of generations for the MCMC.
an evolutionary model: either "BM" or "lambda".
a method: either "reduced" or "full".
a list of control parameters containing the following elements: sig2: starting value for \(\sigma^2\) (BM rate); lambda: starting value for the \(\lambda\) parameter; a: starting for the state at the root node; xbar: starting values for the states at the tips; intV: starting value for the intraspecific variance (reduced method); or v: starting value for the vector of intraspecific variances for all species (full method); pr.mean: means for the prior distributions in the following order - sig2, lambda (if applicable), a, xbar, intV or v (if applicable), note that the prior probability distribution is exponential for sig2 and normal for a and y; pr.var: variances on the prior distributions, same order as pr.mean.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
Revell, L. J. and R. G. Reynolds. (2012) A new Bayesian method for fitting evolutionary models to comparative data with intraspecific variation. Evolution, 66, 2697-2707.
anc.Bayes, brownie.lite, evol.rate.mcmc